Global analysis of protein folding using massively parallel design, synthesis, and testing

Gabriel Rocklin, Tamuka M. Chidyausiku, Inna Goreshnik, Alex Ford, Scott Houliston, Alexander Lemak, Lauren Carter, Rashmi Ravichandran, Vikram K. Mulligan, Aaron Chevalier, Cheryl H. Arrowsmith, David Baker*

*Corresponding author for this work

Research output: Contribution to journalArticle

120 Scopus citations

Abstract

Proteins fold into unique native structures stabilized by thousands of weak interactions that collectively overcome the entropic cost of folding. Although these forces are "encoded" in the thousands of known protein structures, "decoding" them is challenging because of the complexity of natural proteins that have evolved for function, not stability. We combined computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for more than 15,000 de novo designed miniproteins, 1000 natural proteins, 10,000 point mutants, and 30,000 negative control sequences. This analysis identified more than 2500 stable designed proteins in four basic folds-a number sufficient to enable us to systematically examine how sequence determines folding and stability in uncharted protein space. Iteration between design and experiment increased the design success rate from 6% to 47%, produced stable proteins unlike those found in nature for topologies where design was initially unsuccessful, and revealed subtle contributions to stability as designs became increasingly optimized. Our approach achieves the long-standing goal of a tight feedback cycle between computation and experiment and has the potential to transform computational protein design into a data-driven science.

Original languageEnglish (US)
Pages (from-to)168-175
Number of pages8
JournalScience
Volume357
Issue number6347
DOIs
StatePublished - Jul 14 2017

ASJC Scopus subject areas

  • General

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